allpy: 9c00d065c054 utils/freqs.py

allpy

view utils/freqs.py @ 1012:9c00d065c054

structure, ignore_one_ss: fix a crash for alignments of >=3 sequences This bug is caused by multiple addition of ss markup in geometrical_cores(). It did not appear for pair alignment, since geometrical_cores() was called only once. close #143

author	Boris Nagaev <bnagaev@gmail.com>
date	Tue, 06 Mar 2012 19:21:59 +0400
parents	8c7e5c16b2f4
children

line source

1 #!/usr/bin/python

2 """Read alignment on stdin. Print CSV table of letter frequences on stdout.

3 """

4 from allpy import protein

5 from allpy.data import codes

6 import sys

8 sys.stderr.write(__doc__)

10 def freq(monomer):

11 amount = freqs.get(monomer)

12 if amount:

13 return 100.0 * amount / width

14 return ""

16 aln = protein.Alignment().append_file(sys.stdin)

17 monomers = [code1 for code1, modified, _, _ in codes.protein if not modified]

18 monomers += ["-"]

19 width = len(aln.sequences)

20 print ", ".join(map(str, monomers))

21 for column in aln.columns_as_lists():

22 freqs = {}

23 for monomer in column:

24 if monomer:

25 monomer = monomer.code1

26 else:

27 monomer = "-"

28 freqs[monomer] = freqs.get(monomer, 0) + 1

29 print ", ".join(map(str, map(freq, monomers)))